Classifications

• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
  • A61K31/4427—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems
  • A61K31/4439—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. omeprazole
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
  • A61K38/005—Enzyme inhibitors
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/50—Pyridazines; Hydrogenated pyridazines
  • A61K31/502—Pyridazines; Hydrogenated pyridazines ortho- or peri-condensed with carbocyclic ring systems, e.g. cinnoline, phthalazine
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
  • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents

Definitions

• the invention relates to RoIQ inhibitors for use in the treatment of cancer associated with a Shieldin deficiency and to pharmaceutical compositions comprising said RoIQ inhibitors.
• Somatic cells are subject to continuous DNA damage caused by exogenous and endogenous sources.
• the range of processes through which cells sense, signal and repair DNA damage is termed the DNA damage response (DDR).
• DDR DNA damage response
• DSBs can be repaired by one of three main pathways: homologous recombination (HR), non-homologous end-joining (NHEJ) and alternative NHEJ (alt-NHEJ).
• HR-mediated end-joining MMEJ
• HR-mediated repair is a high-fidelity mechanism essential for accurate repair, preventing cancer-predisposing genomic instability (Wood & D.00e DNA Repair (2016), 44, 22-32, Wyatt etal Mol. Cell (2016) 63, 662-673).
• NHEJ and MMEJ are error-prone pathways that can leave mutational scars at the site of repair.
• MMEJ can function in parallel to both HR and NHEJ pathways (Truong etal. PNAS 2013, 110 (19), 7720-7725).
• Normal cells generally direct repair through the error-free HR pathway to repair DSBs. If cells become deficient in HR, they can use end-joining methods to prevent cell death, but this is mutagenic and can ultimately lead to tumourigenesis.
• Shieldin complex was discovered as an important regulator of DSBR pathway choice in a physiological setting. Shieldin components bind to DSB ends, protecting them from the resection machinery required for HR-mediated repair and promoting repair through NHEJ. Loss of Shieldin components were shown to induce resistance to PARP inhibitors in BRCA1 null cells by partially restoring HR.
• a RoIQ inhibitor for use in the treatment of cancer associated with a Shieldin deficiency.
• FIG. 1 Graphs demonstrating the effect of two DNA polymerase theta (RoIQ) inhibitors, Compound A (a) and Compound B (b), and the PARP inhibitor olaparib (c) on the size of parental and C20orf196 knockout (KO) SUM149 tumouroids.
• Figure 3 Graphs demonstrating the effect of two RoIQ inhibitors, Compound A and Compound B, and the PARP inhibitor olaparib on the fraction of dead cells in parental and C20orf196 knockout (KO) SUM149 tumouroid cultures. The data represent mean +
• HCC1937 cells are proficient in classical NHEJ (cNHEJ). An extrachromosomal DNA substrate was transfected into cells and NHEJ-mediated repair was confirmed by PCR (a). A luminescent NHEJ reporter substrate was designed to detect the cellular repair of non-cohesive DSBs by a classical NHEJ mechanism. HCC1937 cells are deleted for SHLD2 as confirmed using qPCR (c). An isogenic panel of HCT116 cells deleted for various cNHEJ genes ( LIG4 , XRCC4 and XLF) were confirmed null for respective proteins by Western blot (d).
• HCC1937 cells were transfected with the substrate outlined in (b) and a Firefly luciferase plasmid (transfection control).
• cNHEJ repair efficiency was expressed as NanoLuciferase luminescence normalised to FireFly luminescence (arbitrary units) in (e) and was robust in HCC1937 cells.
• FIG. 5 Graphs demonstrating the effect of the REV7 knock out (KO) in combination with RoIQ inhibition on the viability of DLD1 colon cancer cells, as shown by a focused CRISPR-Cas9 KO screen
• Position of REV7 and BRCA2 KO are marked on the graph
• FIG. 6 A short interfering (si)RNA screen was carried out in CAL51 breast cancer cell lines to identify genes, that when silenced, caused sensitivity to Compound A. 1280 siRNA SMART pools were used in this screen, each SMART pools silencing a different gene. The effects on Compound A sensitivity are shown in (a) as Drug Effect Z scores. Negative Z scores indicate siRNAs that caused Compound A sensitivity.
• the DE Z-score threshold of -2 (dotted line) was used for defining synthetic lethal interactions; the DE Z scores for three different control, non-targeting, siRNAs in this screen were 1.0 (Allstar control), 0.8 (siCONI) and 1.0 (siCON2).
• Values shown in the figure are medians from triplicate screens (b) Amongst the genes whose siRNAs caused increased sensitivity to Compound A (DE ⁇ -2), siRNA pool targeting REV7 caused sensitivity (DE Z-score of -2.88). Values shown in the figure are medians from triplicate screens.
• Figure 7 Graphs demonstrating the effect of the RoIQ inhibitor Compound A (a), and the PARP inhibitor olaparib (b) on the clonogenic survival (Y axis) of parental and REV7 knockout (KO) 22Rv1 cells.
• the histogram in (c) compares the relative survival of cells treated with 12 mM Compound A or 0.44 pM olaparib.
• the data represent mean ⁇ SEM of a technical triplicate. The experiment is representative of a biological triplicate.
• Figure 8 (a) Scatter plots of Compound A Drug Effect (DE) Z-scores from a siRNA screen where the effect of each of 1418 siRNAs on Compound A sensitivity was assessed in BRCA1 defective RPE1 cells. The screen was performed as described above for the CAL51 siRNA screen (b) Amongst the genes whose siRNAs caused increased sensitivity to Compound A (DE ⁇ -2), multiple different siRNAs targeting either FAM35A or REV7 caused sensitivity. By comparison, the DE Z scores for three different control, non targeting, siRNAs in this screen were 1.3 (Allstar control), -0.8 (siCONI) and -0.6 (siCON2). Values shown in the figure are medians from triplicate screens.
• DE Drug Effect
• FIG. 10 Dose-response clonogenic survival curves of SUM149 Parental and 3 different REV7 KO cell lines exposed to increasing concentrations of Compound A (a) or olaparib (b) for 14 days. Compared to the SUM149 Parental clone, all three REV7 KO clones showed increased sensitivity to Compound A and resistance to the PARP inhibitor, olaparib.
• the REV7 mutation in clone 1 is NM_001127325 1:g.11680401_ 11680415del GTAGACCTCGCGCAC (SEQ ID NO: 3); the REV7 mutation in clone 2 is NM_001127325 1:g.11680393delC; the REV7 mutation in clone 3 is a 3bp deletion that truncates the protein coding sequence.
• FIG 11 Graphs demonstrating the effect of the DNA polymerase theta (RoIQ) inhibitor Compound A, the PARP inhibitor olaparib and the control compound staurosporine on the fraction of dead cells in parental (a) and REV7 knockout (KO) (b) SUM149 tumouroids.
• Figure 12 Graphs demonstrating the effect of the DNA polymerase theta (RoIQ) inhibitor Compound A (a), and the PARP inhibitor olaparib (b) on the clonogenic survival (Y axis) of parental and three SHLD2 KO clones of HCC1395 cells.
• the histogram in (c) compares the relative survival of cells treated with 1.3mM Compound A or 0.03mM olaparib.
• the data represent mean ⁇ SEM of a technical triplicate. The experiment is representative of a biological duplicate.
• Figure 13 Graphs demonstrating the effect of the DNA polymerase theta (RoIQ) inhibitor Compound A (a), and the PARP inhibitor olaparib (b) on the clonogenic survival (Y axis) of parental and three SHLD2 KO clones of MDA-MB-436 cells.
• the histogram in (c) compares the relative survival of cells treated with 0.75mM Compound A or 0.01 mM olaparib.
• the data represent mean ⁇ SEM of a technical triplicate and were generated with Artios CFA protocol.
• Figure 14 Re-sensitisation of Shieldin-defective, PARPi-resistant cells to olaparib after exposure to Compound A for 48 hours.
• Parental SUM 149 cells or derivatives with either BRCA1 restored (SUM 149 Revertant) or with genetic deletion of either C20orf196 (SUM149 C20orf196) or 53BP1 (SUM149 53BP1) were treated with either DMSO or Compound A (10 mM) for 48 hours then re-plated into medium containing either DMSO or olaparib (1 mM) and incubated for a further 10 days. Deletion of C20orf196 or 53BP1 as well as expression of BRCA1 caused marked resistance to olaparib.
• a RoIQ inhibitor for use in the treatment of cancer associated with a Shieldin deficiency.
• a RoIQ inhibitor for use in the treatment of PARP inhibitor resistant cancer.
• said cancer associated with a Shieldin deficiency is also a cancer which is resistant to PARP inhibitors.
• Molecular mechanisms of resistance to PARP inhibitors that have been delineated preclinically include: (i) reactivation of HR through reversion of BRCA1 or BRCA2 mutant alleles by acquiring secondary mutations; (ii) loss of NHEJ components; (iii) loss of Shieldin protein complex components such as 53BP1, rev7, SHLD1, SHLD2, SHLD3; (iv) loss of PARP1 expression; (v) PARP1 mutation; (vi) upregulation of MDR1 drug efflux; (vii) loss of PARG protein expression; (viii) replication fork stabilization; (ix) upregulation of MET or PI3K kinase signaling; and (x) expression of microRNA’s that direct DNA repair pathway choice (Noordermeer etal.
• RoIQ UniProtKB - 075417 (DPOLQ_HUMAN)
• MMEJ Mert - 075417
• RoIQ is a multifunctional enzyme, which comprises an N-terminal helicase domain (SF2 HEL308-type) and a C-terminal low-fidelity DNA polymerase domain (A-type) (Wood & D bountye DNA Repair (2016), 44, 22-32). Both domains have been shown to have concerted mechanistic functions in MMEJ.
• the helicase domain mediates the removal of RPA protein from ssDNA ends and stimulates annealing.
• the polymerase domain extends the ssDNA ends and fills the remaining gaps. Therapeutic inactivation of RoIQ would thus disable the ability of cells to perform MMEJ and provide a novel targeted strategy in an array of defined tumour contexts.
• RoIQ has been shown to be essential for the survival of HRD cells (e.g. synthetic lethal with FA/BRCA-deficiency) and is up-regulated in HRD tumour cell lines (Ceccaldi etal. Nature (2015), 518(7538), 258-262).
• HRD cells e.g. synthetic lethal with FA/BRCA-deficiency
• HRD tumour cell lines Ceccaldi etal. Nature (2015), 518(7538), 258-262
• RoIQ is significantly over expressed in subsets of HRD ovarian, uterine and breast cancers with associated poor prognosis (Higgins etal. Oncotarget (2010), 1, 175-184, Lemee etal. PNAS (2010), 107(30), 13390-13395, Ceccaldi et ai (2015), supra).
• RoIQ is largely absent in normal tissues but has been shown to be upregulated in matched cancer samples thus correlating elevated expression with disease (Kawamura et al. International Journal of Cancer (2004), 109(1), 9-16). Secondly, its suppression or inhibition confers radio-sensitivity in tumour cells. Finally, RoIQ inhibition could conceivably prevent what could be MMEJ-dependent functional reversion of BRCA2 mutations that underlie the emergence of cisplatin and PARP inhibitor resistance in tumours (Dhillon etal. Cancer Sci (2011) 102, 663-669).
• RoIQ As a therapeutic target, it should be noted that the function of RoIQ in MMEJ has only quite recently been discovered (reviewed in Wood & D bountye DNA Repair (2016), 44, 22-32). The present inventors have discovered that the inhibition of RoIQ is selectively lethal to cancer cells that are resistant to PARP inhibition through loss of Shieldin components. This has significant implications for the treatment of cancer patients bearing tumours that are resistant to PARP inhibitor-based therapies.
• Shieldin is a protein complex that ‘shields’ the ends of DNA DSBs from resection - an essential step required for repair by HR - and directs repair through NHEJ (Noordermeer et al. Nature (2016), 560(7716), 117-121, Dev etal. Nature Cell Biology (2016), 20(8), 954-965, Ghezraoui etal Nature (2016) 560 (7716), 122-127, Mirman etal Nature (2016) 560 (7716), 112-116). Loss of the Shieldin complex by depletion or deletion of any of the component parts has been reported to restore DNA end resection and therefore repair by HR. Similar to PARP inhibition, various literature reports have highlighted synthetic lethal interactions between HRD and RoIQ inhibition. It was therefore surprising to discover that although HR restoration through Shieldin loss causes HRD SUM149T cells to become resistant to PARP inhibition, the same cells are selectively sensitive to RoIQ inhibitors.
• said cancer comprises cancer cells which were previously sensitive to PARP inhibitors.
• the cancer may have initially been sensitive to a PARP inhibitor- based therapy, but then subsequently becoming resistant to the PARP inhibitor-based therapy causing the patient to relapse with resistant disease.
• said cancer comprises cancer cells which were initially identified as homologous recombination repair pathway-deficient.
• the cancer initially sensitive to a PARP inhibitor-based therapy may have had a deficient, reduced or abrogated ability to repair its DNA by the process of HR.
• Components of the HR pathway are well characterised and are listed below.
• said deficiency is selected from a deficiency in any one or more of the following genes, or a protein encoded by said genes: ATM, ATR, BRCA1, BRCA2, BARD1, RAD51C, RAD50, CHEK1, CHEK2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, PALB2 (FANCN), FANCP (BTBD12), ERCC4 (FANCQ), PTEN, CDK12, MRE11, NBS1, NBN, CLASPIN, BLM, WRN, SMARCA2, SMARCA4, LIG1 , RPA1, RPA2, BRIP1 and PTEN.
• genes include ATM, ATR, BRCA1, BRCA2, BARD1, RAD51C, RAD50, CHEK1, CHEK2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANC
• references herein to “homologous recombination repair pathway- deficient” or “deficiency in homologous recombination (HRD)” refer to absence, defective expression or any variation of any gene or gene product which results in a deficiency or loss of function of the resultant homologous recombination repair pathway.
• examples of said genetic variation include mutations (e.g. point mutations), substitutions, deletions, single nucleotide polymorphisms (SNPs), haplotypes, chromosome abnormalities, Copy Number Variation (CNV), epigenetics, DNA inversions, reduction in expression and mis-localisation.
• said cancer comprises cancer cells which have subsequently reactivated the homologous recombination repair pathway.
• said deficiency in the homologous recombination repair pathway comprises a Shieldin deficiency.
• the individual will have lost the activity of the Shieldin complex through any means including loss of expression, or mutation or epigenetic silencing of the components of the Shieldin complex.
• Members of the Shieldin complex are well known to those in the field and currently include, but are not limited to, C20orf196 (SHLD1), FAM35A (SHLD2) and CTC-534A2.2 (SHLD3).
• said Shieldin deficiency is a deficiency in any one or more of the following genes, or a protein encoded by said genes: C20orf196 (SHLD1), FAM35A (SHLD2) and CTC-534A2.2 (SHLD3).
• Shieldin deficiency is a deficiency in the 53BP1 complex.
• the 53BP1 complex acts as a NHEJ promoting complex and comprises of TP53BP1 (53BP1), RIF1 and MAD2L2 (REV7).
• said deficiency in the 53BP1 complex comprises a deficiency in any one or more of the following genes, or a protein encoded by said genes: TP53BP1 (53BP1), RIF1 and MAD2L2 (REV7).
• said cancer comprises cancer cells which have become dependent upon microhomology mediated end-joining (MMEJ) for survival.
• MMEJ microhomology mediated end-joining
• Loss of Shieldin has been shown to affect DSBR pathway choice in a physiological setting. By deprotecting blunt DNA ends, disruption of the Shieldin complex causes DNA to be resected, favouring repair through homologous recombination and reducing repair via canonical NHEJ (cNHEJ).
• cNHEJ canonical NHEJ
• the NHEJ pathway is not completely defective, as it is in cells deleted for core NHEJ genes such as LIG4 and XRCC4.
• cancer cells that are SHLD2 deleted can efficiently repair transfected extrachromosomal DSB substrates through NHEJ ( Figure 4). It was therefore surprising that cells deficient in Shieldin genes but that were otherwise competent for NHEJ or HR were sensitive to RoIQ inhibitors. Thus, cells deleted for Shieldin components are not NHEJ deficient.
• RoIQ inhibitor examples include an agent capable of causing a reduction in functional activity of RoIQ, for example a decrease in enzymatic activity which may be partial or complete. ‘RoIQ inhibitor’ also refers to agents that do not affect the intrinsic activity of RoIQ but impair the ability of RoIQ to bind its substrate or cofactor. Partial or complete reduction in the functional activity of RoIQ may induce lethality of growth arrest of cancer cells that are defective in one or more components of the Shieldin pathway.
• Inhibition of functional activity of RoIQ may be through enzymatic inhibition of its polymerase or helicase domain. In one embodiment, inhibition of RoIQ functional activity is through inhibition of the polymerase domain.
• a RoIQ inhibitor useful in the present invention may be a polypeptide, polynucleotide, antibody, peptide, small molecule compound, an inhibitory small interfering RNA molecule or any other suitable chemical.
• a RoIQ inhibitor is a small molecule compound.
• the RoIQ inhibitor is a small molecule compound comprising a heterocyclic amide moiety.
• the RoIQ inhibitor is selected from either of Compounds A or B.
• cancers and their benign counterparts which may be treated (or inhibited) include, but are not limited to tumours of epithelial origin (adenomas and carcinomas of various types including adenocarcinomas, squamous carcinomas, transitional cell carcinomas and other carcinomas) such as carcinomas of the bladder and urinary tract, breast, gastrointestinal tract (including the esophagus, stomach (gastric), small intestine, colon, rectum and anus), liver (hepatocellular carcinoma), gall bladder and biliary system, exocrine pancreas, kidney, lung (for example adenocarcinomas, small cell lung carcinomas, non-small cell lung carcinomas, bronchioalveolar carcinomas and mesotheliomas), head and neck (for example cancers of the tongue, buccal cavity, larynx, pharynx, nasopharynx, tonsil, salivary glands, nasal cavity and paranasal sinuses), ovary, fallopian
• lymphoid lineage for example acute lymphocytic leukemia [ALL], chronic lymphocytic leukemia [CLL], B-cell lymphomas such as diffuse large B-cell lymphoma [DLBCL], follicular lymphoma, Burkitt’s lymphoma, mantle cell lymphoma, MALT lymphoma, T-cell lymphomas and leukaemias, natural killer [NK] cell lymphomas, Hodgkin’s lymphomas, hairy cell leukaemia, monoclonal gammopathy of uncertain significance, plasmacytoma, multiple myeloma, and post-transplant lymphoproliferative disorders), and haematological malignancies and related conditions of myeloid lineage (for example acute myelogenous leukemia [AML], chronic myelogenous leukemia [CML], chronic
• Metastasis or metastatic disease is the spread of a disease from one organ or part to another non-adjacent organ or part.
• the cancers which can be treated by the compounds of the invention include primary tumours (i.e. cancer cells at the originating site), local invasion (cancer cells which penetrate and infiltrate surrounding normal tissues in the local area), and metastatic (or secondary) tumours ie. tumours that have formed from malignant cells which have circulated through the bloodstream (haematogenous spread) or via lymphatics or across body cavities (trans-coelomic) to other sites and tissues in the body.
• cancers include hepatocellular carcinoma, melanoma, oesophageal, renal, colon, colorectal, lung e.g. mesothelioma or lung adenocarcinoma, breast, bladder, gastrointestinal, ovarian and prostate cancers.
• the cancer initially sensitive to a PARP inhibitor-based therapy may have been a recurrent epithelial ovarian, fallopian tube or primary peritoneal cancer, which was in complete or partial response to platinum-based chemotherapy.
• the active compound While it is possible for the active compound to be administered alone, it is preferable to present it as a pharmaceutical composition (e.g. formulation). In one embodiment this is a sterile pharmaceutical composition.
• the present invention further provides pharmaceutical compositions, as defined above, and methods of making a pharmaceutical composition comprising (e.g admixing) at least one compound, together with one or more pharmaceutically acceptable excipients and optionally other therapeutic or prophylactic agents, as described herein.
• the pharmaceutically acceptable excipient(s) can be selected from, for example, carriers (e.g. a solid, liquid or semi-solid carrier), adjuvants, diluents, fillers or bulking agents, granulating agents, coating agents, release-controlling agents, binding agents, disintegrants, lubricating agents, preservatives, antioxidants, buffering agents, suspending agents, thickening agents, flavouring agents, sweeteners, taste masking agents, stabilisers or any other excipients conventionally used in pharmaceutical compositions.
• carriers e.g. a solid, liquid or semi-solid carrier
• adjuvants e.g. a solid, liquid or semi-solid carrier
• pharmaceutically acceptable refers to compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of a subject (e.g. human) without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
• a subject e.g. human
• Each carrier, excipient, etc. must also be “acceptable” in the sense of being compatible with the other ingredients of the formulation.
• compositions containing compounds can be formulated in accordance with known techniques, see for example, Remington’s Pharmaceutical Sciences, Mack Publishing Company, Easton, PA, USA.
• compositions can be in any form suitable for oral, parenteral, topical, intranasal, intrabronchial, sublingual, ophthalmic, otic, rectal, intra-vaginal, or transdermal administration.
• compositions are intended for parenteral administration, they can be formulated for intravenous, intramuscular, intraperitoneal, subcutaneous administration or for direct delivery into a target organ or tissue by injection, infusion or other means of delivery.
• the delivery can be by bolus injection, short term infusion or longer term infusion and can be via passive delivery or through the utilisation of a suitable infusion pump or syringe driver.
• compositions adapted for parenteral administration include aqueous and non- aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats, co-solvents, surface active agents, organic solvent mixtures, cyclodextrin complexation agents, emulsifying agents (for forming and stabilizing emulsion formulations), liposome components for forming liposomes, gellable polymers for forming polymeric gels, lyophilisation protectants and combinations of agents for, inter alia, stabilising the active ingredient in a soluble form and rendering the formulation isotonic with the blood of the intended recipient.
• aqueous and non- aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats, co-solvents, surface active agents, organic solvent mixtures, cyclodextrin complexation agents, emulsifying agents (for forming and stabilizing emulsion formulations), liposome components for forming liposomes, gellable poly
• compositions for parenteral administration may also take the form of aqueous and non- aqueous sterile suspensions which may include suspending agents and thickening agents (R. G. Strickly, Solubilizing Excipients in oral and injectable formulations, Pharmaceutical Research, Vol 21(2) 2004, p 201-230).
• the formulations may be presented in unit-dose or multi-dose containers, for example sealed ampoules, vials and prefilled syringes, and may be stored in a freeze-dried (lyophilised) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use.
• the formulation is provided as an active pharmaceutical ingredient in a bottle for subsequent reconstitution using an appropriate diluent.
• the pharmaceutical formulation can be prepared by lyophilising the compound, or sub groups thereof. Lyophilisation refers to the procedure of freeze-drying a composition. Freeze-drying and lyophilisation are therefore used herein as synonyms.
• Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets.
• compositions of the present invention for parenteral injection can also comprise pharmaceutically acceptable sterile aqueous or non-aqueous solutions, dispersions, suspensions or emulsions as well as sterile powders for reconstitution into sterile injectable solutions or dispersions just prior to use.
• aqueous and nonaqueous carriers, diluents, solvents or vehicles examples include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), carboxymethylcellulose and suitable mixtures thereof, vegetable oils (such as sunflower oil, safflower oil, corn oil or olive oil), and injectable organic esters such as ethyl oleate.
• polyols such as glycerol, propylene glycol, polyethylene glycol, and the like
• carboxymethylcellulose and suitable mixtures thereof examples include vegetable oils (such as sunflower oil, safflower oil, corn oil or olive oil), and injectable organic esters such as ethyl oleate.
• vegetable oils such as sunflower oil, safflower oil, corn oil or olive oil
• injectable organic esters such as ethyl oleate.
• Proper fluidity can be maintained, for example, by the use of thickening or coating materials such as lecit
• compositions of the present invention may also contain adjuvants such as preservatives, wetting agents, emulsifying agents, and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol, sorbic acid, and the like. It may also be desirable to include agents to adjust tonicity such as sugars, sodium chloride, and the like. Prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as aluminum monostearate and gelatin.
• the pharmaceutical composition is in a form suitable for i.v. administration, for example by injection or infusion.
• the solution can be dosed as is, or can be injected into an infusion bag (containing a pharmaceutically acceptable excipient, such as 0.9% saline or 5% dextrose), before administration.
• the pharmaceutical composition is in a form suitable for sub-cutaneous (s.c.) administration.
• Pharmaceutical dosage forms suitable for oral administration include tablets (coated or uncoated), capsules (hard or soft shell), caplets, pills, lozenges, syrups, solutions, powders, granules, elixirs and suspensions, sublingual tablets, wafers or patches such as buccal patches.
• tablet compositions can contain a unit dosage of active compound together with an inert diluent or carrier such as a sugar or sugar alcohol, eg; lactose, sucrose, sorbitol or mannitol; and/or a non-sugar derived diluent such as sodium carbonate, calcium phosphate, calcium carbonate, or a cellulose or derivative thereof such as microcrystalline cellulose (MCC), methyl cellulose, ethyl cellulose, hydroxypropyl methyl cellulose, and starches such as corn starch.
• Tablets may also contain such standard ingredients as binding and granulating agents such as polyvinylpyrrolidone, disintegrants (e.g.
• swellable crosslinked polymers such as crosslinked carboxymethylcellulose
• lubricating agents e.g. stearates
• preservatives e.g. parabens
• antioxidants e.g. BHT
• buffering agents for example phosphate or citrate buffers
• effervescent agents such as citrate/bicarbonate mixtures.
• excipients are well known and do not need to be discussed in detail here. Tablets may be designed to release the drug either upon contact with stomach fluids (immediate release tablets) or to release in a controlled manner (controlled release tablets) over a prolonged period of time or with a specific region of the Gl tract.
• Capsule formulations may be of the hard gelatin or soft gelatin variety and can contain the active component in solid, semi-solid, or liquid form.
• Gelatin capsules can be formed from animal gelatin or synthetic or plant derived equivalents thereof.
• the solid dosage forms can be coated or un-coated. Coatings may act either as a protective film (e.g. a polymer, wax or varnish) or as a mechanism for controlling drug release or for aesthetic or identification purposes.
• the coating e.g. a Eudragit TM type polymer
• the coating can be designed to release the active component at a desired location within the gastro-intestinal tract.
• the coating can be selected so as to degrade under certain pH conditions within the gastrointestinal tract, thereby selectively release the compound in the stomach or in the ileum, duodenum, jejenum or colon.
• the drug can be presented in a solid matrix comprising a release controlling agent, for example a release delaying agent which may be adapted to release the compound in a controlled manner in the gastrointestinal tract.
• a release controlling agent for example a release delaying agent which may be adapted to release the compound in a controlled manner in the gastrointestinal tract.
• the drug can be presented in a polymer coating e.g. a polymethacrylate polymer coating, which may be adapted to selectively release the compound under conditions of varying acidity or alkalinity in the gastrointestinal tract.
• the matrix material or release retarding coating can take the form of an erodible polymer (e.g. a maleic anhydride polymer) which is substantially continuously eroded as the dosage form passes through the gastrointestinal tract.
• the coating can be designed to disintegrate under microbial action in the gut.
• the active compound can be formulated in a delivery system that provides osmotic control of the release of the compound. Osmotic release and other delayed release or sustained release formulations (for example formulations based on ion exchange resins) may be prepared in accordance with methods well known to those skilled in the art.
• the compound may be formulated with a carrier and administered in the form of nanoparticles, the increased surface area of the nanoparticles assisting their absorption.
• nanoparticles offer the possibility of direct penetration into the cell.
• Nanoparticle drug delivery systems are described in “Nanoparticle Technology for Drug Delivery”, edited by Ram B Gupta and Uday B. Kompella, Informa Healthcare, ISBN 9781574448573, published 13 th March 2006. Nanoparticles for drug delivery are also described in J. Control. Release, 2003, 91 (1-2), 167-172, and in Sinha et al., Mol. Cancer Ther. August 1, (2006) 5, 1909.
• the pharmaceutical compositions typically comprise from approximately 1% (w/w) to approximately 95% (w/w) active ingredient and from 99% (w/w) to 5% (w/w) of a pharmaceutically acceptable excipient or combination of excipients. Particularly, the compositions comprise from approximately 20% (w/w) to approximately 90%,% (w/w) active ingredient and from 80% (w/w) to 10% of a pharmaceutically acceptable excipient or combination of excipients.
• the pharmaceutical compositions comprise from approximately 1% to approximately 95%, particularly from approximately 20% to approximately 90%, active ingredient.
• Pharmaceutical compositions according to the invention may be, for example, in unit dose form, such as in the form of ampoules, vials, suppositories, pre-filled syringes, dragees, tablets or capsules.
• the pharmaceutically acceptable excipient(s) can be selected according to the desired physical form of the formulation and can, for example, be selected from diluents (e.g solid diluents such as fillers or bulking agents; and liquid diluents such as solvents and co solvents), disintegrants, buffering agents, lubricants, flow aids, release controlling (e.g. release retarding or delaying polymers or waxes) agents, binders, granulating agents, pigments, plasticizers, antioxidants, preservatives, flavouring agents, taste masking agents, tonicity adjusting agents and coating agents.
• diluents e.g solid diluents such as fillers or bulking agents; and liquid diluents such as solvents and co solvents
• disintegrants e.g solid diluents such as fillers or bulking agents
• lubricants such as solvents and co solvents
• flow aids e.g. release retarding or de
• tablets and capsules typically contain 0-20% disintegrants, 0-5% lubricants, 0-5% flow aids and/or 0-99% (w/w) fillers/ or bulking agents (depending on drug dose). They may also contain 0-10% (w/w) polymer binders, 0-5% (w/w) antioxidants, 0-5% (w/w) pigments. Slow release tablets would in addition contain 0-99% (w/w) release-controlling (e.g. delaying) polymers (depending on dose).
• the film coats of the tablet or capsule typically contain 0-10% (w/w) polymers, 0-3% (w/w) pigments, and/or 0-2% (w/w) plasticizers.
• Parenteral formulations typically contain 0-20% (w/w) buffers, 0-50% (w/w) cosolvents, and/or 0-99% (w/w) Water for Injection (WFI) (depending on dose and if freeze dried).
• WFI Water for Injection
• Formulations for intramuscular depots may also contain 0-99% (w/w) oils.
• compositions for oral administration can be obtained by combining the active ingredient with solid carriers, if desired granulating a resulting mixture, and processing the mixture, if desired or necessary, after the addition of appropriate excipients, into tablets, dragee cores or capsules. It is also possible for them to be incorporated into a polymer or waxy matrix that allow the active ingredients to diffuse or be released in measured amounts.
• the compounds of the invention can also be formulated as solid dispersions.
• Solid dispersions are homogeneous extremely fine disperse phases of two or more solids.
• Solid solutions molecularly disperse systems
• one type of solid dispersion are well known for use in pharmaceutical technology (see (Chiou and Riegelman, J. Pharm. Sci. , 60, 1281- 1300 (1971)) and are useful in increasing dissolution rates and increasing the bioavailability of poorly water-soluble drugs.
• Solid dosage forms include tablets, capsules, chewable tablets and dispersible or effervescent tablets.
• Known excipients can be blended with the solid solution to provide the desired dosage form.
• a capsule can contain the solid solution blended with (a) a disintegrant and a lubricant, or (b) a disintegrant, a lubricant and a surfactant.
• a capsule can contain a bulking agent, such as lactose or microcrystalline cellulose.
• a tablet can contain the solid solution blended with at least one disintegrant, a lubricant, a surfactant, a bulking agent and a glidant.
• a chewable tablet can contain the solid solution blended with a bulking agent, a lubricant, and if desired an additional sweetening agent (such as an artificial sweetener), and suitable flavours.
• Solid solutions may also be formed by spraying solutions of drug and a suitable polymer onto the surface of inert carriers such as sugar beads (‘non-pareils’). These beads can subsequently be filled into capsules or compressed into tablets.
• the pharmaceutical formulations may be presented to a patient in “patient packs” containing an entire course of treatment in a single package, usually a blister pack.
• Patient packs have an advantage over traditional prescriptions, where a pharmacist divides a patient’s supply of a pharmaceutical from a bulk supply, in that the patient always has access to the package insert contained in the patient pack, normally missing in patient prescriptions.
• the inclusion of a package insert has been shown to improve patient compliance with the physician’s instructions.
• compositions for topical use and nasal delivery include ointments, creams, sprays, patches, gels, liquid drops and inserts (for example intraocular inserts). Such compositions can be formulated in accordance with known methods.
• formulations for rectal or intra-vaginal administration include pessaries and suppositories which may be, for example, formed from a shaped moldable or waxy material containing the active compound. Solutions of the active compound may also be used for rectal administration.
• compositions for administration by inhalation may take the form of inhalable powder compositions or liquid or powder sprays, and can be administrated in standard form using powder inhaler devices or aerosol dispensing devices. Such devices are well known.
• the powdered formulations typically comprise the active compound together with an inert solid powdered diluent such as lactose.
• a formulation may contain from 1 nanogram to 2 grams of active ingredient, e.g. from 1 nanogram to 2 milligrams of active ingredient. Within these ranges, particular sub-ranges of compound are 0.1 milligrams to 2 grams of active ingredient (more usually from 10 milligrams to 1 gram, e.g. 50 milligrams to 500 milligrams), or 1 microgram to 20 milligrams (for example 1 microgram to 10 milligrams, e.g. 0.1 milligrams to 2 milligrams of active ingredient).
• a unit dosage form may contain from 1 milligram to 2 grams, more typically 10 milligrams to 1 gram, for example 50 milligrams to 1 gram, e.g. 100 miligrams to 1 gram, of active compound.
• the active compound will be administered to a patient in need thereof (for example a human or animal patient) in an amount sufficient to achieve the desired therapeutic effect.
• a method of treating cancer associated with a Shieldin deficiency which comprises administering a RoIQ inhibitor to a patient in need thereof.
• the compounds are generally administered to a subject in need of such administration, for example a human or animal patient, particularly a human.
• the compounds will typically be administered in amounts that are therapeutically or prophylactically useful and which generally are non-toxic. However, in certain situations (for example in the case of life threatening diseases), the benefits of administering the compound may outweigh the disadvantages of any toxic effects or side effects, in which case it may be considered desirable to administer compounds in amounts that are associated with a degree of toxicity.
• the compounds may be administered over a prolonged term to maintain beneficial therapeutic effects or may be administered for a short period only. Alternatively they may be administered in a continuous manner or in a manner that provides intermittent dosing (e.g. a pulsatile manner).
• a typical daily dose of the compound can be in the range from 100 picograms to 100 milligrams per kilogram of body weight, more typically 5 nanograms to 25 milligrams per kilogram of bodyweight, and more usually 10 nanograms to 15 milligrams per kilogram (e.g. 10 nanograms to 10 milligrams, and more typically 1 microgram per kilogram to 20 milligrams per kilogram, for example 1 microgram to 10 milligrams per kilogram) per kilogram of bodyweight although higher or lower doses may be administered where required.
• the compound can be administered on a daily basis or on a repeat basis every 2, or 3, or 4, or 5, or 6, or 7, or 10 or 14, or 21, or 28 days for example.
• the compounds may be administered orally in a range of doses, for example 1 to 1500 mg,
• the compound may be administered once or more than once each day.
• the compound can be administered continuously (i.e. taken every day without a break for the duration of the treatment regimen).
• the compound can be administered intermittently (i.e. taken continuously for a given period such as a week, then discontinued for a period such as a week and then taken continuously for another period such as a week and so on throughout the duration of the treatment regimen).
• treatment regimens involving intermittent administration include regimens wherein administration is in cycles of one week on, one week off; or two weeks on, one week off; or three weeks on, one week off; or two weeks on, two weeks off; or four weeks on two weeks off; or one week on three weeks off - for one or more cycles, e.g. 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more cycles.
• a patient will be given an infusion of the compound for periods of one hour daily for up to ten days in particular up to five days for one week, and the treatment repeated at a desired interval such as two to four weeks, in particular every three weeks. More particularly, a patient may be given an infusion of the compound for periods of one hour daily for 5 days and the treatment repeated every three weeks.
• a patient is given an infusion over 30 minutes to 1 hour followed by maintenance infusions of variable duration, for example 1 to 5 hours, e.g. 3 hours.
• a patient is given a continuous infusion for a period of 12 hours to 5 days, an in particular a continuous infusion of 24 hours to 72 hours.
• a patient is given the compound orally once a week.
• a patient is given the compound orally once-daily for between 7 and 28 days such as 7, 14 or 28 days.
• a patient is given the compound orally once-daily for 1 day, 2 days, 3 days, 5 days or 1 week followed by the required amount of days off to complete a one or two week cycle.
• a patient is given the compound orally once-daily for 2 weeks followed by 2 weeks off.
• a patient is given the compound orally once-daily for 2 weeks followed by 1 week off.
• a patient is given the compound orally once-daily for 1 week followed by 1 week off.
• the quantity of compound administered and the type of composition used will be commensurate with the nature of the disease or physiological condition being treated and will be at the discretion of the physician.
• RoIQ inhibitors can be used as a single agent or in combination with other anticancer agents. Combination experiments can be performed, for example, as described in Chou TC, Talalay P. Quantitative analysis of dose-effect relationships: the combined effects of multiple drugs or enzyme inhibitors. Adv Enzyme Regulat 1984;22: 27- 55.
• the compounds as defined herein can be administered as the sole therapeutic agent or they can be administered in combination therapy with one of more other compounds (or therapies) for treatment of a particular disease state, for example a neoplastic disease such as a cancer as hereinbefore defined.
• the compounds of the invention may be advantageously employed in combination with one or more other medicinal agents, more particularly, with other anti-cancer agents or adjuvants (supporting agents in the therapy) in cancer therapy.
• Examples of other therapeutic agents or treatments that may be administered together (whether concurrently or at different time intervals) with the compounds include but are not limited to:
• anti-cancer agents or adjuvants include but are not limited to any of the agents selected from groups (i)-(xlvii), and optionally group (xlviii), below:
• Platinum compounds for example cisplatin (optionally combined with amifostine), carboplatin or oxaliplatin;
• Taxane compounds for example paclitaxel, paclitaxel protein bound particles (AbraxaneTM), docetaxel, cabazitaxel or larotaxel;
• Topoisomerase I inhibitors for example camptothecin compounds, for example camptothecin, irinotecan(CPT11), SN-38, or topotecan;
• Topoisomerase II inhibitors for example anti-tumour epipodophyllotoxins or podophyllotoxin derivatives for example etoposide, or teniposide;
• Vinca alkaloids for example vinblastine, vincristine, liposomal vincristine (Onco-TCS), vinorelbine, vindesine, vinflunine or vinvesir;
• Nucleoside derivatives for example 5-fluorouracil (5-FU, optionally in combination with leucovorin), gemcitabine, capecitabine, tegafur, UFT, S1, cladribine, cytarabine (Ara-C, cytosine arabinoside), fludarabine, clofarabine, or nelarabine;
• Antimetabolites for example clofarabine, aminopterin, or methotrexate, azacitidine, cytarabine, floxuridine, pentostatin, thioguanine, thiopurine, 6-mercaptopurine, or hydroxyurea (hydroxycarbamide);
• Alkylating agents such as nitrogen mustards or nitrosourea, for example cyclophosphamide, chlorambucil, carmustine (BCNU), bendamustine, thiotepa, melphalan, treosulfan, lomustine (CCNU), altretamine, busulfan, dacarbazine, estramustine, fotemustine, ifosfamide (optionally in combination with mesna), pipobroman, procarbazine, streptozocin, temozolomide, uracil, mechlorethamine, methylcyclohexylchloroethylnitrosurea, or nimustine (ACNU);
• nitrogen mustards or nitrosourea for example cyclophosphamide, chlorambucil, carmustine (BCNU), bendamustine, thiotepa, melphalan, treosulfan, lomustine (CCNU), altretamine
• Anthracyclines, anthracenediones and related drugs for example daunorubicin, doxorubicin (optionally in combination with dexrazoxane), liposomal formulations of doxorubicin (eg. CaelyxTM, MyocetTM, DoxilTM), idarubicin, mitoxantrone, epirubicin, amsacrine, or valrubicin;
• Epothilones for example ixabepilone, patupilone, BMS-310705, KOS-862 and ZK-EPO, epothilone A, epothilone B, desoxyepothilone B (also known as epothilone D or KOS- 862), aza-epothilone B (also known as BMS-247550), aulimalide, isolaulimalide, or luetherobin;
• DNA methyl transferase inhibitors for example temozolomide, azacytidine or decitabine, or SGI-110;
• Antifolates for example methotrexate, pemetrexed disodium, or raltitrexed
• Cytotoxic antibiotics for example antinomycin D, bleomycin, mitomycin C, dactinomycin, carminomycin, daunomycin, levamisole, plicamycin, or mithramycin;
• Tubulin-binding agents for example combrestatin, colchicines or nocodazole;
• EGFR epidermal growth factor receptor
• VEGFR vascular endothelial growth factor receptor
• PDGFR platelet-derived growth factor receptor
• MTKI multi target kinase inhibitors
• Raf inhibitors mTOR inhibitors for example imatinib mesylate, erlotinib, gefitinib, dasatinib, lapatinib, dovotinib, axitinib, nilotinib, vandetanib, vatalinib, pazopanib, sorafenib, sunitinib, temsirolimus, everolimus (RAD 001), vemurafenib (PLX4032/RG7204), dabrafenib, encorafenib or an IKB kinase inhibitor such as SAR- 113945, bardox
• Aurora kinase inhibitors for example AT9283, barasertib (AZD1152), TAK-901, MK0457 (VX680), cenisertib (R-763), danusertib (PHA-739358), alisertib (MLN-8237), or MP- 470;
• CDK inhibitors for example AT7519, roscovitine, seliciclib, alvocidib (flavopiridol), dinaciclib (SCH-727965), 7-hydroxy-staurosporine (UCN-01), JNJ-7706621, BMS- 387032 (a.k.a. SNS-032), PHA533533, PD332991 , ZK-304709, or AZD-5438;
• AKT inhibitors such as KRX-0401 (perifosine/ NSC 639966), ipatasertib (GDC-0068; RG-7440), afuresertib (GSK-2110183; 2110183), MK-2206, MK-8156, AT13148, AZD-5363, triciribine phosphate (VQD-002; triciribine phosphate monohydrate (API-2; TCN-P; TCN-PM; VD- 0002), RX-0201, NL-71-101 , SR-13668, PX-316, AT13148, AZ-5363, Semaphore, SF1126, or Enzastaurin HCI (LY317615) or MTOR inhibitors such as rapamycin analogues such as RAD 001 (everolimus), CCI 779 (temsirolemus), AP
• CBP-501 forkhead translocation inhibitors
• enzastaurin HCI LY317615
• PI3K Inhibitors such as dactolisib (BEZ235), buparlisib (BKM-120; NVP- BKM-120), BYL719, copanlisib (BAY-80-6946), ZSTK-474, CUDC-907, apitolisib (G DC- 0980; RG-7422), pictilisib (pictrelisib, GDC-0941, RG-7321), GDC-0032, GDC-0068, GSK-2636771, idelalisib (formerly CAL-101, GS 1101, GS-1101), MLN1117 (INK1117), MLN0128 (INK128), IPI-145 (INK1197), LY-3023414, ipatasertib, afuresertib, MK-2206, MK
• Hsp90 inhibitors for example AT13387, herbimycin, geldanamycin (GA), 17-allylamino- 17-desmethoxygeldanamycin (17-AAG) e.g. NSC-330507, Kos-953 and CNF-1010, 17- dimethylaminoethylamino-17-demethoxygeldanamycin hydrochloride (17-DMAG) e.g. NSC-707545 and Kos-1022, NVP-AUY922 (VER-52296), NVP-BEP800, CNF-2024
• Monoclonal Antibodies (unconjugated or conjugated to radioisotopes, toxins or other agents), antibody derivatives and related agents, such as anti-CD, anti-VEGFR, anti- HER2, anti-CTLA4, anti-PD-1 or anti-EGFR antibodies, for example rituximab (CD20), ofatumumab (CD20), ibritumomab tiuxetan (CD20), GA101 (CD20), tositumomab (CD20), epratuzumab (CD22), lintuzumab (CD33), gemtuzumab ozogamicin (CD33), alemtuzumab (CD52), galiximab (CD80), trastuzumab (HER2 antibody), pertuzumab (HER2), trastuzumab-DM1 (HER2), ertumaxomab (HER2 and CD3), cetuximab (EGFR), panitum,
• Estrogen receptor antagonists or selective estrogen receptor modulators (SERMs) or inhibitors of estrogen synthesis for example tamoxifen, fulvestrant, toremifene, droloxifene, faslodex, or raloxifene;
• Aromatase inhibitors and related drugs such as exemestane, anastrozole, letrazole, testolactone aminoglutethimide, mitotane or vorozole;
• Antiandrogens i.e. androgen receptor antagonists
• related agents for example bicalutamide, nilutamide, flutamide, cyproterone, or ketoconazole;
• Hormones and analogues thereof such as medroxyprogesterone, diethylstilbestrol (a.k.a. diethylstilboestrol) or octreotide;
• Steroids for example dromostanolone propionate, megestrol acetate, nandrolone (decanoate, phenpropionate), fluoxymestrone or gossypol;
• CYP17 Steroidal cytochrome P450 17alpha-hydroxylase-17,20-lyase inhibitor
• GnRAs Gonadotropin releasing hormone agonists or antagonists
• Glucocorticoids for example prednisone, prednisolone, dexamethasone;
• Differentiating agents such as retinoids, rexinoids, vitamin D or retinoic acid and retinoic acid metabolism blocking agents (RAMBA) for example accutane, alitretinoin, bexarotene, or tretinoin;
• RAMBA retinoic acid metabolism blocking agents
• Chromatin targeted therapies such as histone deacetylase (HDAC) inhibitors for example panobinostat, resminostat, abexinostat, vorinostat, romidepsin, belinostat, entinostat, quisinostat, pracinostat, tefinostat, mocetinostat, givinostat, CU DC-907, CUDC-101, ACY-1215, MGCD-290, EVP-0334, RG-2833, 4SC-202, romidepsin, AR-42 (Ohio State University), CG-200745, valproic acid, CKD-581, sodium butyrate, suberoylanilide hydroxamide acid (SAHA), depsipeptide (FR 901228), dacinostat (NVP- LAQ824), R306465/ JNJ-16241199, JNJ-26481585, trichostatin A, chlamydocin
• HDAC
• Radiolabelled drugs for radioimmunotherapy for example with a beta particle-emitting isotope (e.g. Iodine -131, Yittrium-90) or an alpha particle-emitting isotope (e.g., Bismuth-213 or Actinium-225) for example ibritumomab or Iodine tositumomab;
• a beta particle-emitting isotope e.g. Iodine -131, Yittrium-90
• an alpha particle-emitting isotope e.g., Bismuth-213 or Actinium-225
• interferons such as interferon-g and interferon a
• interleukins e.g. interleukin 2
• aldesleukin denileukin diftitox
• interferon alfa 2a interferon alfa 2b
• peginterferon alfa 2b peginterferon alfa 2b
• Therapeutic Vaccines such as sipuleucel-T (Provenge) or OncoVex;
• Cytokine-activating agents include Picibanil, Romurtide, Sizofiran, Virulizin, or Thymosin;
• (xliv) Enzymes such as L-asparaginase, pegaspargase, rasburicase, or pegademase;
• DNA repair inhibitors such as PARP inhibitors for example, olaparib, velaparib, iniparib, rucaparib (AG-014699 or PF-01367338), talazoparib or AG-014699;
• DNA damage response inhibitors such as ATM inhibitors AZD0156 MS3541, ATR inhibitors AZD6738, M4344, M6620 wee1 inhibitor AZD1775;
• Agonists of Death receptor e.g. TNF-related apoptosis inducing ligand (TRAIL) receptor
• TRAIL TNF-related apoptosis inducing ligand
• mapatumumab previously HGS-ETR1
• conatumumab formerly AMG 655
• PRO95780 lexatumumab
• dulanermin CS-1008
• apomab recombinant TRAIL ligands
• recombinant Human TRAIL/Apo2 Ligand recombinant Human TRAIL/Apo2 Ligand
• Prophylactic agents i.e. agents that reduce or alleviate some of the side effects associated with chemotherapy agents, for example
• - agents that prevent or decrease the duration of chemotherapy-associated neutropenia and prevent complications that arise from reduced levels of platelets, red blood cells or white blood cells, for example interleukin-11 (e.g. oprelvekin), erythropoietin (EPO) and analogues thereof (e.g. darbepoetin alfa), colony- stimulating factor analogs such as granulocyte macrophage-colony stimulating factor (GM-CSF) (e.g. sargramostim), and granulocyte-colony stimulating factor (G-CSF) and analogues thereof (e.g. filgrastim, pegfilgrastim),
• interleukin-11 e.g. oprelvekin
• EPO erythropoietin
• analogues thereof e.g. darbepoetin alfa
• colony- stimulating factor analogs such as granulocyte macrophage-colony stimulating factor (GM-CSF) (e
• - agents that inhibit bone resorption such as denosumab or bisphosphonates e.g. zoledronate, zoledronic acid, pamidronate and ibandronate,
• agents used to reduce blood levels of growth hormone and IGF-I (and other hormones) in patients with acromegaly or other rare hormone-producing tumours such as synthetic forms of the hormone somatostatin e.g. octreotide acetate,
• agents for pain e.g. opiates such as morphine, diamorphine and fentanyl,
• NSAID non-steroidal anti-inflammatory drugs
• COX-2 inhibitors for example celecoxib, etoricoxib and lumiracoxib
• agents for mucositis e.g. palifermin
• agents for the treatment of side-effects including anorexia, cachexia, oedema or thromoembolic episodes, such as megestrol acetate.
• the anticancer is selected from recombinant interferons (such as interferon-g and interferon a) and interleukins (e.g. interleukin 2), for example aldesleukin, denileukin diftitox, interferon alfa 2a, interferon alfa 2b, or peginterferon alfa 2b; interferon-a2 (500 m/ml) in particular interferon-b; and signal transduction inhibitors such as kinase inhibitors (e.g.
• EGFR epidermal growth factor receptor
• VEGFR vascular endothelial growth factor receptor
• PDGFR platelet-derived growth factor receptor
• MTKI multi target kinase inhibitors
• Raf inhibitors mTOR inhibitors for example imatinib mesylate, erlotinib, gefitinib, dasatinib, lapatinib, dovotinib, axitinib, nilotinib, vandetanib, vatalinib, pazopanib, sorafenib, sunitinib, temsirolimus, everolimus (RAD 001), vemurafenib (PLX4032/RG7204), dabrafenib, encorafenib or an IKB kinase inhibitor such as SAR-113945, bardoxolone, BMS-066, BMS-345541, IMD-0354, IKB kinase inhibitor such as
• each of the compounds present in the combinations of the invention may be given in individually varying dose schedules and via different routes.
• the posology of each of the two or more agents may differ: each may be administered at the same time or at different times.
• a person skilled in the art would know through his or her common general knowledge the dosing regimes and combination therapies to use.
• the compound of the invention may be using in combination with one or more other agents which are administered according to their existing combination regimen. Examples of standard combination regimens are provided below.
• the taxane compound is advantageously administered in a dosage of 50 to 400 mg per square meter (mg/m 2 ) of body surface area, for example 75 to 250 mg/m 2 , particularly for paclitaxel in a dosage of about 175 to 250 mg/m 2 and for docetaxel in about 75 to 150 mg/m 2 per course of treatment.
• the camptothecin compound is advantageously administered in a dosage of 0.1 to 400 mg per square meter (mg/m 2 ) of body surface area, for example 1 to 300 mg/m 2 , particularly for irinotecan in a dosage of about 100 to 350 mg/m 2 and for topotecan in about 1 to 2 mg/m 2 per course of treatment.
• the anti-tumour podophyllotoxin derivative is advantageously administered in a dosage of 30 to 300 mg per square meter (mg/m 2 ) of body surface area, for example 50 to 250mg/m 2 , particularly for etoposide in a dosage of about 35 to 100 mg/m 2 and for teniposide in about 50 to 250 mg/m 2 per course of treatment.
• the anti-tumour vinca alkaloid is advantageously administered in a dosage of 2 to 30 mg per square meter (mg/m 2 ) of body surface area, particularly for vinblastine in a dosage of about 3 to 12 mg/m 2 , for vincristine in a dosage of about 1 to 2 mg/m 2 , and for vinorelbine in dosage of about 10 to 30 mg/m 2 per course of treatment.
• the anti-tumour nucleoside derivative is advantageously administered in a dosage of 200 to 2500 mg per square meter (mg/m 2 ) of body surface area, for example 700 to 1500 mg/m 2 , particularly for 5-FU in a dosage of 200 to 500mg/m 2 , for gemcitabine in a dosage of about 800 to 1200 mg/m 2 and for capecitabine in about 1000 to 2500 mg/m 2 per course of treatment.
• the alkylating agents such as nitrogen mustard or nitrosourea is advantageously administered in a dosage of 100 to 500 mg per square meter (mg/m 2 ) of body surface area, for example 120 to 200 mg/m 2 , particularly for cyclophosphamide in a dosage of about 100 to 500 mg/m 2 , for chlorambucil in a dosage of about 0.1 to 0.2 mg/kg, for carmustine in a dosage of about 150 to 200 mg/m 2 , and for lomustine in a dosage of about 100 to 150 mg/m 2 per course of treatment.
• mg/m 2 body surface area
• cyclophosphamide in a dosage of about 100 to 500 mg/m 2
• chlorambucil in a dosage of about 0.1 to 0.2 mg/kg
• carmustine in a dosage of about 150 to 200 mg/m 2
• lomustine in a dosage of about 100 to 150 mg/m 2 per course of treatment.
• the anti-tumour anthracycline derivative is advantageously administered in a dosage of 10 to 75 mg per square meter (mg/m 2 ) of body surface area, for example 15 to 60 mg/m 2 , particularly for doxorubicin in a dosage of about 40 to 75 mg/m 2 , for daunorubicin in a dosage of about 25 to 45mg/m 2 , and for idarubicin in a dosage of about 10 to 15 mg/m 2 per course of treatment.
• the antiestrogen agent is advantageously administered in a dosage of about 1 to 100 mg daily depending on the particular agent and the condition being treated.
• Tamoxifen is advantageously administered orally in a dosage of 5 to 50 mg, particularly 10 to 20 mg twice a day, continuing the therapy for sufficient time to achieve and maintain a therapeutic effect.
• Toremifene is advantageously administered orally in a dosage of about 60mg once a day, continuing the therapy for sufficient time to achieve and maintain a therapeutic effect.
• Anastrozole is advantageously administered orally in a dosage of about 1mg once a day.
• Droloxifene is advantageously administered orally in a dosage of about 20-1 OOmg once a day.
• Raloxifene is advantageously administered orally in a dosage of about 60mg once a day.
• Exemestane is advantageously administered orally in a dosage of about 25mg once a day.
• Antibodies are advantageously administered in a dosage of about 1 to 5 mg per square meter (mg/m 2 ) of body surface area, or as known in the art, if different.
• Trastuzumab is advantageously administered in a dosage of 1 to 5 mg per square meter (mg/m 2 ) of body surface area, particularly 2 to 4mg/m 2 per course of treatment.
• the compounds can be administered simultaneously or sequentially.
• the two or more compounds will be administered within a period and in an amount and manner that is sufficient to ensure that an advantageous or synergistic effect is achieved.
• they can be administered at closely spaced intervals (for example over a period of 5-10 minutes) or at longer intervals (for example 1, 2, 3, 4 or more hours apart, or even longer periods apart where required), the precise dosage regimen being commensurate with the properties of the therapeutic agent(s).
• These dosages may be administered for example once, twice or more per course of treatment, which may be repeated for example every 7, 14, 21 or 28 days.
• the compound for the manufacture of a medicament for use in therapy wherein said compound is used in combination with one, two, three, or four other therapeutic agents.
• a medicament for treating cancer which comprises the compound wherein said medicament is used in combination with one, two, three, or four other therapeutic agents.
• the invention further provides use of the compound for the manufacture of a medicament for enhancing or potentiating the response rate in a patient suffering from a cancer where the patient is being treated with one, two, three, or four other therapeutic agents.
• the weight ratio of the compound according to the present invention and the one or more other anticancer agent(s) when given as a combination may be determined by the person skilled in the art. Said ratio and the exact dosage and frequency of administration depends on the particular compound according to the invention and the other anticancer agent(s) used, the particular condition being treated, the severity of the condition being treated, the age, weight, gender, diet, time of administration and general physical condition of the particular patient, the mode of administration as well as other medication the individual may be taking, as is well known to those skilled in the art. Furthermore, it is evident that the effective daily amount may be lowered or increased depending on the response of the treated subject and/or depending on the evaluation of the physician prescribing the compounds of the instant invention. A particular weight ratio for the compound and another anticancer agent may range from 1/10 to 10/1 , more in particular from 1/5 to 5/1, even more in particular from 1/3 to 3/1.
• the compounds of the invention may also be administered in conjunction with non- chemotherapeutic treatments such as radiotherapy, photodynamic therapy, gene therapy; surgery and controlled diets.
• non- chemotherapeutic treatments such as radiotherapy, photodynamic therapy, gene therapy; surgery and controlled diets.
• the compounds of the present invention also have therapeutic applications in sensitising tumour cells for radiotherapy and chemotherapy.
• the compounds of the present invention can be used as "radiosensitizer” and/or “chemosensitizer” or can be given in combination with another "radiosensitizer” and/or “chemosensitizer”.
• the compound of the invention is for use as chemosensitiser.
• radiosensitizer is defined as a molecule administered to patients in therapeutically effective amounts to increase the sensitivity of the cells to ionizing radiation and/or to promote the treatment of diseases which are treatable with ionizing radiation.
• chemosensitizer is defined as a molecule administered to patients in therapeutically effective amounts to increase the sensitivity of cells to chemotherapy and/or promote the treatment of diseases which are treatable with chemotherapeutics.
• the compound of the invention is administered with a "radiosensitizer” and/or “chemosensitizer”. In one embodiment the compound of the invention is administered with an "immune sensitizer”.
• immune sensitizer is defined as a molecule administered to patients in therapeutically effective amounts to increase the sensitivity of cells to a RoIQ inhibitor.
• radiosensitizers include, but are not limited to, the following: metronidazole, misonidazole, desmethylmisonidazole, pimonidazole, etanidazole, nimorazole, mitomycin C, RSU 1069, SR 4233, E09, RB 6145, nicotinamide, 5- bromodeoxyuridine (BUdR), 5- iododeoxyuridine (lUdR), bromodeoxycytidine, fluorodeoxyuridine (FudR), hydroxyurea, cisplatin, and therapeutically effective analogs and derivatives of the same.
• Photodynamic therapy (PDT) of cancers employs visible light as the radiation activator of the sensitizing agent.
• photodynamic radiosensitizers include the following, but are not limited to: hematoporphyrin derivatives, Photofrin, benzoporphyrin derivatives, tin etioporphyrin, pheoborbide-a, bacteriochlorophyll-a, naphthalocyanines, phthalocyanines, zinc phthalocyanine, and therapeutically effective analogs and derivatives of the same.
• Radiosensitizers may be administered in conjunction with a therapeutically effective amount of one or more other compounds, including but not limited to: compounds of the invention; compounds which promote the incorporation of radiosensitizers to the target cells; compounds which control the flow of therapeutics, nutrients, and/or oxygen to the target cells; chemotherapeutic agents which act on the tumour with or without additional radiation; or other therapeutically effective compounds for treating cancer or other diseases.
• Chemosensitizers may be administered in conjunction with a therapeutically effective amount of one or more other compounds, including but not limited to: compounds of the invention; compounds which promote the incorporation of chemosensitizers to the target cells; compounds which control the flow of therapeutics, nutrients, and/or oxygen to the target cells; chemotherapeutic agents which act on the tumour or other therapeutically effective compounds for treating cancer or other disease.
• Calcium antagonists for example verapamil, are found useful in combination with antineoplastic agents to establish chemosensitivity in tumor cells resistant to accepted chemotherapeutic agents and to potentiate the efficacy of such compounds in drug-sensitive malignancies.
• immune sensitizers include the following, but are not limited to: immunomodulating agents, for example monoclonal antibodies such as immune checkpoint antibodies [e.g. CTLA-4 blocking antibodies and/or antibodies against PD-1 and PD-L1 and/or PD-L2 for example ipilimumab (CTLA4), MK-3475 (pembrolizumab, formerly lambrolizumab, anti-PD-1), nivolumab (anti-PD-1), BMS-936559 (anti- PD-L1), MPDL320A, AMP-514 or MEDI4736 (anti-PD-L1), or tremelimumab (formerly ticilimumab, CP-675,206, anti-CTLA-4)]; or Signal Transduction inhibitors; or cytokines (such as recombinant interferons); or oncolytic viruses; or immune adjuvants (e.g. BCG).
• immunomodulating agents for example monoclonal antibodies such as immune checkpoint antibodies
• Immune sensitizers may be administered in conjunction with a therapeutically effective amount of one or more other compounds, including but not limited to: compounds of the invention; compounds which promote the incorporation of immune sensitizers to the target cells; compounds which control the flow of therapeutics, nutrients, and/or oxygen to the target cells; therapeutic agents which act on the tumour or other therapeutically effective compounds for treating cancer or other disease.
• the compound and one, two, three, four or more other therapeutic agents can be, for example, formulated together in a dosage form containing two, three, four or more therapeutic agents i.e. in a unitary pharmaceutical composition containing all agents.
• the individual therapeutic agents may be formulated separately and presented together in the form of a kit, optionally with instructions for their use.
• a PI3K/AKT pathway inhibitor selected from: apitolisib, buparlisib, Copanlisib, pictilisib, ZSTK- 474, CUDC-907, GSK-2636771 , LY-3023414, ipatasertib, afuresertib, MK
• the compound in combination with one or more (e.g. 1 or 2) other therapeutic agents (e.g. anticancer agents) for use in therapy, such as in the prophylaxis or treatment of cancer.
• one or more e.g. 1 or 2
• other therapeutic agents e.g. anticancer agents
• the pharmaceutical composition comprises the compound together with a pharmaceutically acceptable carrier and optionally one or more therapeutic agent(s).
• the invention relates to the use of a combination according to the invention in the manufacture of a pharmaceutical composition for inhibiting the growth of tumour cells.
• the invention relates to a product containing the compound and one or more anticancer agent, as a combined preparation for simultaneous, separate or sequential use in the treatment of patients suffering from cancer.
• Shieldin loss represents an effective RoIQ inhibitor patient selection biomarker in an HR-proficient setting (see Examples 5 to 7 and Figures 5 to 7).
• Shieldin loss represents an effective RoIQ inhibitor patient selection biomarker in an HR-deficient and PARP-resistant setting (see Examples 8 to 12 and Figures 8 to 12).
• Shieldin loss represents an effective RoIQ inhibitor patient selection biomarker in an HR-deficient and PARP-sensitive setting (see Example 13 and Figure 13.
• Cells were cultured under normal growth conditions (37°C, 5% CO2), and passaged at 80% confluency. All cell lines are listed in Table 1 with their tissue origin, homologous recombination (HR) status, culture medium and source.
• HR homologous recombination
• HR Homologous Recombination
• FBS Foetal Bovine Serum
• C20orf196 SUM 149 cells are a derivative of SUM 149 that have a genetic deletion of the Shieldin component C20orf196 (SHLD1) (Noordermeer et al Nature (2016) 560, 117-121 /Asterand).
• SHLD1 Shieldin component C20orf196
• SUM149 breast cancer cells and the derivative SUM149 cell line, C20orf196 SUM149 were cultured under normal growth conditions (37°C, 5% CO2) and passaged at 80% confluency.
• Growth medium consisted of Ham’s F-12 medium (Gibco) supplemented with 5% heat- inactivated foetal bovine serum (FBS) (Sigma-Aldrich), 10pg/mL insulin (Sigma-Aldrich), 0.5pg/ml_ hydrocortisone (Sigma-Aldrich) and penicillin / streptomycin (Gibco).
• REV7 KO and SHLD2 KO clones in MDA-MB-436, HCC1395 and 22Rv1 cell lines were generated by Oxford Genetics as described in their pipeline. Briefly, synthetic guide RNAs (sgRNA) for CRISPR/Cas9 were designed to specifically target a key coding exon of the gene of interest. Pools of cells carrying the edited gene were generated by transient co transfection of the sgRNA complexed with CRISPR/Cas9 protein. Single cells were isolated, and the targeted exon was sequenced by Sanger sequencing. Selected clones with out-of- frame insertion/deletions in all alleles were expanded and validated by PCR followed by high-throughput sequencing. The loss of REV7 protein was also validated by Western blot. One REV7 KO 22Rv1 clone and three SHLD2 KO HCC1395 and MDA-MB-436 clones were generated.
• sgRNA synthetic guide RNAs
• test compounds and olaparib were added in an eight- point dose range with a one in three serial dilution (maximum concentration 12mM for all compounds, except 30mM compound A for REV7 KO cell experiments).
• Dimethyl sulfoxide (DMSO) and 1mM staurosporine (Med Chem Express) treatments were included as negative and positive controls, respectively. All treatments were carried out in quadruplicate.
• the extrachromosomal MMEJ/NHEJ assay DNA substrate was generated as described in Wyatt etal (Mol. Cell (2016) 63, 662-673) to generate a DNA molecule comprising a central dsDNA region flanked by 45 nucleotide ssDNA overhangs with a terminal, complementary 4nt microhomologies.
• the reporter detecting cNHEJ-mediated repair of a non-cohesive DSB ( Figure 4) is based on the “EJ5” reporter described in Bennardo et al PLoS Genet (2008) 4(6):e1000110.
• the GFP open reading frame has been replaced by NanoLuciferase (Promega) and the l-Scel recognition sites flanking the DSB have opposing polarity to ensure that they are not complementary and require cellular processing to be ligated.
• the construct was synthesised by GeneWiz and subcloned into pcDNA5/FRT using existing 5' Kpn ⁇ and 3' Xho ⁇ restriction sites.
• the transfection-ready substrate was generated by l-Scel digestion and gel purification (Qiagen).
• the transfection-ready substrate comprises an EcoRV-excised blunt end fragment separated from the vector backbone by agarose gel electrophoresis and purified by gel extraction (Qiagen).
• the EcoRV site is within the NanoLuciferase open reading frame and thus requires cNHEJ-mediated ligation without end processing to maintain an intact ORF after cellular repair.
• the assay was performed as described in Wyatt etal (Mol. Cell (2016) 63, 662-673), with modifications to use lipid-mediated transfection of the DNA substrate. 500,000 HCC1937 cells were incubated with 0.1% DMSO at 37°C in loosely capped 15 ml tubes. Cells were then transfected with 500ng FireFly luciferase plasmid and 2.5pg MMEJ/NHEJ DNA substrate. Transfection was carried out by lipofection with JetPRIME (Polyplus), according to manufacturer’s instructions. Briefly, DNA and transfection reagent were mixed at a 1pg:2pL ratio in 200pL transfection buffer and incubated for 10 minutes at room temperature before adding to cells.
• Transfected cells were seeded in a 6 well plate, in a final volume of 2m L media containing 0.1% DMSO, and incubated at 37°C for 24h. Cells were harvested by trypsinisation, and washed once with PBS. Cells were then incubated in 12.5U/mL benzonase in HBSS for 15 minutes at 37°C. Cells were washed twice in PBS. Genomic DNA was extracted using the DNA Mini Kit (Qiagen) as per the manufacturer’s instructions. To detect MMEJ, PCR was carried out using the KOD Hotstart Polymerase Kit (Merck) as per manufacturer’s instructions.
• Cells were harvested by trypsinisation, washed with DPBS (PAN Biotech), resuspended in fresh media, and counted. 200,000 cells were centrifuged at 400 x g for five minutes and resuspended in 20mI_ supplemented SE nucleofection solution (Lonza) containing the NanoLuciferase DNA substrate and FireFly luciferase plasmid (Promega).
• the ratio of reporter substrate to control plasmid was 1pg NanoLuciferase substrate: 400ng FireFly plasmid.
• the ratio was 103.9ng NanoLuciferase substrate: 400ng FireFly plasmid.
• Cells were transferred to a cuvette, electroporated using programme EN-113 (HCT 116) or EN-138 (HCC1937) on the 4D nucleofector X unit (Lonza) and recovered into fresh media to a final density of 250,000 cells/mL. 20,000 cells (80pL of suspension) were seeded per well in a white 96-well microplate (Costar 3610) and incubated for 24 hours at 37°C.
• NanoLuciferase levels were detected using the Nano-Glo® Dual-Luciferase® Reporter Assay system (Promega) as per the manufacturer’s instructions, and luminescence was measured with a Clariostar plate reader (BMG Labtech), using the manufacturer’s protocols ‘FireFly’ and ‘NanoLuciferase’. In each well the NanoLuciferase signal was normalised to the Firefly signal, which served as a measure of both cell density and transfection efficiency.
• HCT116 cells were lysed in standard Laemmli buffer, boiled at 100°C for 10 minutes, and mechanically sheared using a 27G needle. Protein concentration was measured using the BCA assay (Thermo). Lysates were combined with protein loading dye (Life Technologies) containing b-mercaptoethanol and electrophoresed on a 4-12% Bis-Tris Protein Gel (Thermo) at 150 V for 70 minutes. Proteins were transferred onto a 0.2 pm nitrocellulose membrane (Thermo) using the iBIot 2 Gel Transfer Device (Thermo) and pre-set program P3. Total protein was visualized by a brief incubation in Ponceau S (Sigma) and imaged in the Amersham AI600 Imager.
• Membranes were incubated in TBS buffer containing 0.1% Tween 20 (TBST) containing 5% BSA for 2 hours at room temperature, then primary antibody overnight at 4°C. Membranes were washed twice in TBST, then incubated in secondary antibody for 1 hour at room temperature. Membranes were washed four times in TBST, overlaid with ECL detection reagent (GE Healthcare), and exposed in the Amersham AI600 Imager.
• LIG4 Abeam ab193353
• XLF Abeam ab33499
• XRCC4 SCBT sc-271087
• goat-anti-mouse IgG-HRP Thermo 31430
• goat-anti-rabbit IgG-HRP Thermo 31460
• Primary and secondary antibodies were diluted 1:1000 and 1:2000 in 5% BSA, respectively.
• the CRISPR KO screen, sample preparation and data analysis were performed by Horizon Discovery using a CRISPR library against 1965 genes with 10 gRNA’s per gene.
• DLD-1 colon cancer cells were grown in RPMI medium with 10% FBS, infected with the lentiviral library (each viral particle containing Cas9 and sgRNA), selected with puromycin for 2 weeks, and treated with compound B (EC17.1%) or DMSO for 15 days. Synthetic lethality scores were calculated by normalizing the sgRNA count from compound treated cells to DMSO treated control.
• Real-Time Q-PCR was carried out using Applied Biosystems assays in a VNA7 Real-Time PCR system according to manufacturer protocols. Briefly, cell pellets were collected, and RNA was extracted using the RNeasy Plus Mini kit (Qiagen) according to manufacturer’s instructions. Reverse transcription and PCR amplification reactions contained 30ng of RNA in a 10mI reaction in a 384 well plate, using the Luna Universal Probe One-Step RT-qPCR kit (NEB) and the gene-specific Taqman Q-PCR amplification probe-sets (Applied Biosystems) listed in Table 3. The PCR reaction was carried out using the protocol outlined in Table 4. FAM- (test gene) and a VIC- (housekeeping) labelled assays were multiplexed in the same well.
• the data was analyzed with QuantStudio Real Time PCR software to calculate the CT (cycle threshold) value for each gene.
• the delta CT was calculated as CT of the test gene minus CT of the housekeeping gene.
• the relative expression was calculated as 2 A (-delta CT) multiplied by 100 to represent the expression of the test gene as a percentage of the expression of the housekeeping gene.
• siRNA library was purchased from Dharmacon. Each well contained a SMART pool of four distinct siRNA species targeting different sequences of the target transcript, as well as individual siRNA targeting components of the Shieldin complex. Each plate was supplemented with negative siCONTROL (12 wells; Dharmacon) and positive control (four wells, siPLKI, Dharmacon). RNAi screening conditions were optimized and raw CellTitre-Glo (Promega) luminescent viability readings were generated as previously described (Lord etal DNA Repair (2008) 7, 2010-2019).
• Example 1 Effect of RoIQ and PARP inhibitors on the size of parental and C20orf196 KO SUM149 tumouroids
• siRNA screen using 1280 siRNAs was performed using CAL51 breast cancer cells.
• the cells were transfected with siRNA SMARTPools in a 384 well plate arrayed format then, twenty-four hours later, exposed to either DMSO or Compound A.
• Cells were then continuously cultured in the presence of Compound A or DMSO for a further five days, at which point the viability of cells was measured using CellTitre-Glo reagent (a luminescence assay measuring cellular ATP levels).
• Luminescence values from each well of the 384 well plate were log2 transformed and then normalized to the median signal on each plate (to account for plate to plate variation).
• REV7 KO 22Rv1 cells are significantly more sensitive to RoIQ inhibitor (Compound A, in a and left panels of c) compared to REV7 wild type 22Rv1 parental cells, as evidenced by a decreased relative survival in the REV7 KO cells.
• REV7 KO 22Rv1 cells still retain resistance to a PARP inhibitor (olaparib, in b and right panels of c), as evidenced by a similar surviving fraction in REV7 wild type and REV7 KO cells.
• siRNA screen using 1418 siRNAs was performed using BRCA1 defective RPE1 TP53-/- BRCA1-/- cells. The screen was performed and analysed as described in Figure 8 for the CAL51 screen.
• REV7 and SHLD2 were two of the top hits ( Figure 8 (a)), confirming the link between SHLD component defects and RoIQ inhibitor sensitivity.
• Parental or C20orf196 KO SUM 149 cells were seeded into 6 well plates and incubated overnight. The cells were then exposed to a serial dilution of RoIQ inhibitor or olaparib for 14 days, fixed, and stained with sulphorhodamine B. The colonies in each well were counted and normalised survival data plotted to generate a dose-response curve, as described before.
• Parental or REV7 KO SUM 149 cells were seeded into 6 well plates and incubated overnight. The cells were then treated with a serial dilution of RoIQ inhibitor or olaparib for 14 days, fixed, and stained with sulphorhodamine B. The colonies in each well were counted and normalised survival data plotted to generate a dose-response curve.
• HCC1395 is a BRCA1 deficient breast cancer cell line.
• the results presented in Figure 12 show that SHLD2 KO HCC1395 cells are significantly more sensitive to the RoIQ inhibitor Compound A (a and left panels of c) than parental HCC1395 cells, as evidenced by a decreased relative survival. Additionally, SHLD2 KO HCC1395 cells are significantly more resistant to the PARP inhibitor olaparib (b and right panels of c) than parental HCC1395 cells, as evidenced by an increased relative survival.
• Example 13 Effect of RoIQ and PARP inhibitors on survival of parental and SHLD2 KO MDA-MB- 436 cells.
• MDA-MB-436 is a BRCA1 deficient breast cancer cell line.
• the results presented in Figure 13 show that SHLD2 KO MDA-MB-436 cells are significantly more sensitive to RoIQ inhibitor (Compound A, in a and left panels of c) than parental MDA-MB-436 cells, as evidenced by a decreased relative survival.
• a trend for increased resistance of SHLD2 KO MDA-MB-436 to a PARP inhibitor (olaparib, in b and right panels of c) is also observed, as evidenced by an increased relative survival.
• DNA RoIQ inhibitor Compound A restore sensitivity to olaparib in Shieldin- defective, PARPi-resistant SUM 149 cells was determined.

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